Biological Advancement
by The Passionate Admiral
Summary: AU of the infamous episode Threshold. Suppose that everything didn't go back to normal at the end of the episode. J/P Romance, definitely!
1. Enhanced

Biological Advancement

Author: The Passionate Admiral

Rating: T

Disclaimer: I don't own Star Trek: Voyager.

Plot: An AU outcome of the episode which is regarded by many as the "epitome of failure" of the series. Suppose that "Threshold" had happened differently at the end (I know that this one has been done a few times before, but who cares?)

Captain Kathryn Janeway sat on one of the bio-beds in sickbay. Her chief helmsman, Lieutenant Tom Paris, lay on the adjoining bio-bed.

The two of them had been through an ordeal. First Tom had broken the Warp 10 Threshold, then he died, came back to life, and mutated into a different lifeform. Soon after, he had kidnapped Captain Janeway in his mutated form and used the threshold to bring her to a nearby planet. There they had become giant lizard-like organisms, and they had... mated with each other and reproduced.

The two officers were rescued by the crew of the _Voyager_ shortly after, but the offspring had been left behind. Not long after this, Janeway and Paris had been returned to their human form.

Less than 24 hours later, they were back in sickbay being examined for residual side-effects of the threshold disaster. What The Doctor discovered was rather peculiar.

The holographic physician ran the medical tricorder over the vessel's CO. He gave the occasional "Hmmm..." as he observed her. Kes stood by the door, documenting a few reports.

After about five minutes, Captain Janeway started to get annoyed. She said "Doctor, if you don't mind, I'd like to get back to the bridge TODAY."

"Of course, Captain," said the EMH, "There's just something rather peculiar that is going on in your neural pathways."

"What do you mean?" asked Janeway.

"I'm not sure," said The Doctor, "But if I were to venture a guess, I would say-"

"I know you're bored too, Lieutenant," Janeway interrupted him, "But there's no need to complain."

Tom looked over at her, somewhat confused. "Captain, I wasn't complaining."

"I thought I just heard you say 'Hurry up, you babbling cluster of photons,'" said Janeway.

"Well, I freely admit that I may have been thinking that," said Tom, "But I haven't spoken a word since we got here."

"I can vouch for him, Captain," said Kes, looking over her shoulder. "He's been totally silent since I began to examine you."

"That's odd," said Kathryn, "I'm not sure how to say this, but I think I can... sense Tom's thoughts."

"Really?" Tom raised an eyebrow in interest, "What am I thinking now?"

"You're thinking..." Janeway began, but then said "A moment ago, I could sense your thoughts, but now I can't. However, I can tell that you are experiencing fascination."

The Doctor began to examine Captain Janeway's neural pathways again, and finally, he found the solution. He said "Captain, I believe that somehow, through the threshold incident, you have become empathic."

"What?" Janeway stared at the EMH.

"Cool," said Tom, "But empaths can only sense emotions. How was the Captain able to read my mind?"

"It would appear that at certain intervals, she can experience telepathy as well for a certain amount of time," The Doctor reported, going over his results.

"How is that possible?" said Kes.

"Alas, I don't know," The Doctor admitted. Soon, another figure on the tricorder caught his attention. He went over to the wall and pressed a few buttons. He walked back over to the bio-bed and instructed Janeway to stand up. Once she was on her feet, The Doctor said "Captain, I want you to try to pick me up."

"Doctor?" said the confused Captain.

"I need you to do this in order to confirm my theory," said The Doctor.

Janeway shrugged, put her arms around The Doctor's waist and lifted him up easily.

"I must say, you're heavier than I thought you would be." said Janeway.

"That's because I just increased my metric mass to 200 pounds," said The Doctor.

Janeway put The Doctor back down. "How is that possible?" she asked.

"Captain, your strength has been affected as well," the EMH revealed. "Based on these results, I would estimate that you are about three times stronger than the average woman your age."

Tom whistled in amazement. Janeway was too stunned to speak.

The Doctor completed his examination on the Captain and went on to examine the Chief Conn Officer.

Janeway could sense that Tom was no longer feeling bored. To the contrary, he was full of excitement.

"Well, Doc, how have I been affected?" Paris asked after ten minutes.

"Mr. Paris," said The Doctor, "It would appear as though your neural pathways have been affected as well."

"In what way?" asked Kes.

The Doctor spoke with a hint of interest in his voice "I have never seen brain activity like this before. Your neural pathways are taking in information and processing and storing it at an exponential rate!"

"So, basically, you're telling me that somehow through the threshold incident, my awareness, comprehension, and memory have all been improved?" said Tom.

"It's more than just that," said The Doctor. "Mr. Paris, you may as well be the smartest person on board this ship!"

Tom was deeply impressed by the news The Doctor was giving him. He asked him "Doc, do you still weigh 200 pounds?"

"Yes."

"Kes, could you come over here for a moment?" the pilot asked the petite Ocampa.

The blonde alien walked over to his bio-bed. Tom asked her "How much do you weigh?"

"About 90 pounds," she told him.

Tom got up and told her "Hold on to The Doctor for a moment."

Kes wrapped her arms around the EMH. Tom stood in front of them, wrapped his arms around them both, and lifted them both off the ground.

Captain Janeway raised an eyebrow in amazement. Evidently, Tom's strengh had also been increased.

After fifteen seconds, Tom set the Ocampa and the EMH down.

"I don't know why, but I feel like doing back-flips right now." said Tom.

Without warning, he threw himself backward, touched the ground with his hands, and landed standing straight up.

"I probably don't even need to tell you about the changes in Mr. Paris' strength and agility, do I?" asked The Doctor.

"No, I don't see any need to," said Janeway.


	2. A Personal Conversation

The following afternoon, Captain Janeway and Lieutenant Paris were back at their posts on the bridge. The initial shock of their new abilities soon set in. At first, they had planned to keep the knowledge of the matter confidential until further notice. However, knowing how hard it was to keep a secret on that ship, they decided to just go ahead and announce it. Needless to say, everyone was deeply amazed by their new capabilities.

At any rate, Janeway and Paris were back on the bridge. Captain Janeway was at her chair. Commander Chakotay smirked at her, which signified that he was glad that she had not suffered any dismal side-effects from the threshold incient. He had told her that it would have been terrible if she had been rendered "unfit to command," and his supposed reasoning was that "he couldn't handle all the paperwork if the job of CO had been given to him."

Tom sat at the helm. One would think that he engrossed in piloting the ship, but he had other things on his mind. He felt a certain form of frustration and anger coming over him.

It wasn't long before Captain Janeway sensed his emotions. She could tell that something was bothering her chief pilot. She asked him "Is there something on your mind, Lieutenant Paris?"

Tom looked over his shoulder for a moment. Then he turned around completely, stood up, and walked over to the Captain. He stood about three feet in front of her, put his arms behind his back, and said "Captain, I wish to speak to you in your ready room."

She looked up at him and asked "Why can't you speak to me out here on the bridge?"

"What I have to say is of a private... and a personal matter," said Tom. "I would feel uncomfortable to describe it out here."

Janeway understood his reasoning, stood up, and said "Very well. Chakotay, you have the bridge."

Paris looked over his shoulder and said "Pablo, take over." Ensign Baytart walked over to the helm and sat down there to fill in for Tom.

The two of them walked into the ready room. Captain Janeway walked over to the replicator and said "Coffee; black."

After her favorite beverage appeared, she took it and sat at her desk. Gesturing to the chairs in front of the desk, she told her pilot "Please, sit down."

"I'm sure you know I prefer to remain standing," Tom said straightforwardly.

Janeway took a sip of her coffee and asked him "What would you like to talk about?"

"I'm sure you know that, too," he said. "It's about something that happened while you and I were in our lizard-like forms on that planet."

"What about that?" she asked.

"As The Doctor told us, we had mated and reproduced," said Tom. "Do you remember that part?"

"Yes, I can remember everything," Janeway said with a little uneasiness in her voice, "Most of it is blurred, but I can still remember it all."

"I can, too." Tom decided to get straight to the point. He leaned forward, placed his hands on the edge of Janeway's desk to support himself, and asked "Captain, do you actually believe it was prudent to just leave the offspring behind?"

Now Janeway realized why Paris wanted to be alone to talk with her. "Tom, neither you nor I had any say in that matter at the time."

"Captain, they may have been lizards," said Paris, "But they were still lifeforms. For all we know, they will die without someone to care for them."

"Tom, you're not suggesting that we go back, are you?" queried Janeway. "Because if you are, I should inform you that we can't."

"Why not?" said Tom. "If it's because they're lizards, don't worry about that. I'm sure that we'd be able to find a way to turn them into humans."

"That's not the main reason, Tom." Janeway explained. She turned to the monitor on her desk and pressed a few buttons. Then she turned it toward her helmsman. As he studied it, she told him "This starchart shows the region of space that contains the planet the crew found us on. This is what it looked like five minutes after they found us."

Janeway pressed a few more buttons. The image was then flooded with numerous orange dots. Kathryn looked back up at Tom and said "Based upon what our long-range instruments tell us, this is what that region looks like currently."

"The Kazon," Tom muttered in frustration.

The Captain nodded and said "They arrived in the area shortly after the crew recovered us."

"Someone must have tipped them off," Tom concluded. "What of the offspring? Are they safe?"

"It would seem that way," said Janeway, "The Kazon have not set foot on the planet yet. They've only been in orbit."

Tom started rubbing his chin. Janeway could tell that he was in deep thought. After five minutes of deep thinking, Tom asked her "About how far away are we from the planet?"

Janeway looked over the charts, and told him "We're about four light-years away."

Tom grinned and informed her "I have an idea on how to recover the offspring without returning to the planet."

"Really?" Janeway raised an eyebrow. "How?"

He just smiled and told her "Meet me tonight in Transporter Room 1 at 2100 hours. I'll show you then."

Tom turned around and walked back onto the bridge. He relieved Baytart of the post and returned to piloting the ship. Kathryn soon returned to her chair, and not another word was spoken between her and Tom until 2100 hours.


	3. The Three Little Wonders

That night at 2055 hours, Captain Janeway walked out of her quarters on Deck 3 and went to the nearest turbolift. She stepped inside of it and said "Deck Four."

The turbolift went down one deck, and there Janeway got off. She approached Transporter Room 1. The doors opened up for her and she stepped inside. As she had anticipated, Tom was there. But he was not alone; Ensign Harry Kim was with him. Harry was standing on the transporter pad, and Tom was leaning against the front of the transporter console. Janeway did not notice this right away, but Harry had three standard pattern enhancers lying at his feet. The two men had been talking with each other, but both fell silent upon the arrival of their CO.

"Good evening, Captain," they greeted their captain.

"I see that Tom dragged you into this, too, Harry," Janeway commented, smirking slightly.

"He seems very sure that his plan will work." Harry grinned.

"What plan?" inquired Janeway.

"I'll show you," said Tom. He took one step forward. Then in one swift move, he backflipped over the console. He landed flat on his feet right in front of the main panel.

"Can you teach me how to do that?" Harry asked eagerly.

"Perhaps I could when you get back," said Tom.

"'Get back?'" said Janeway. "What are you talking about?"

Paris ignored her. His attention was focused on the main transporter panel. He looked up at his best friend and asked him very sternly "Do you trust me, Harry?"

Harry nodded in complete confidence. "I'm ready whenever you are."

"Good," Tom entered the proper code, and Janeway watched as Harry and the pattern enhancers were beamed off the pad.

She almost immediately tapped her combadge and said "Janeway to Lieutenant Torres!"

"Torres here," the half-Klingon Chief Engineer responded over the line.

"B'Elanna, initiate an all-stop!" Janeway said hastily.

"Right away, Captain!" B'Elanna had her crew cut all power to the warp drive. Once the _Voyager _was at zero velocity, Janeway tapped her combadge again and said "Computer, locate Ensign Harry Kim!"

The computer responded "Ensign Kim is not onboard the _Voyager_."

Janeway tapped her badge for the third time and contacted the bridge, "Janeway to Tuvok."

"Tuvok here, Captain," replied the Vulcan Security Chief, "Is there a problem?"

"Lieutenant Paris just beamed Ensign Kim off the ship!" Janeway informed him. "How close is the nearest planet?"

"I would estimate approximately... 1.03 light-years," said Tuvok. After a pause, he said "Captain, I should inform you that that distance is well outside of transporter range."

Janeway glared back at Tom and asked him very coldly "Where is he, Mr. Paris?"

Tom remained completely calm. He said "Come see for yourself, Captain."

Janeway slowly stepped up to the transporter console. Then she saw why Tom was acting so calmly.

"I beamed Harry to the surface of the planet we left the offspring on," he enlightened her, "In fact, assuming they're right where we left them, he's standing right next to them."

"How is that possible?" said the bewildered Captain Janeway. "We're more than five light-years away from the planet."

"It's simple, Captain," Tom explained, "I just widened the range of the transporter by making a few modifications to its central mechanism. No one's ever made these modifications before because to do so would be rendered 'too risky.' Fortunately, I managed to bypass all the complications completely by compensating with the surplus energy from the auxiliary replicators."

Janeway was speechless to say the least. "Smart thinking, Lieutenant."

"Actually, Captain, some of the credit goes to you," Tom smiled at her.

"Me?"

"You gave me the idea to use the auxiliary replicator energy when you ordered coffee in your ready room," Tom explained.

"I see," Janeway acknowledged. There was a brief silence. Kathryn broke it when she said "What do we do now?"

"Now we go to sickbay," Tom instructed her. "From there, I'll widen the range of my combadge so that we can communicate with Harry."

Later...

On the planet, Harry had located the offspring. He had managed to carry them up onto the surface, but with a little difficulty, as their bodies were very slippery. Once he managed to get all three of them, he set up the pattern enhancers in the shape of a triangle. After that, all he could do was wait.

A moment later, his combadge chirped. "Paris to Kim."

Harry tapped it and said "Kim here."

"Is everything set, Harry?" inquired Tom.

"Yeah, the pattern enhancers are in place," Harry reported. "I found all three of the offspring."

"Good," Harry heard Janeway's voice, "Beam him back, Lieutenant."

"Yes ma'am," was the last thing Harry heard before he was encompassed by the transporter beam.

...

Harry materialized in sickbay. The offspring and the pattern enhancers were at his side. Harry, Kes, and The Doctor each picked up one of the offspring and deposited them onto one of the bio-beds.

"Alright, now that that's over with, I could use a hot shower." said Harry. "Captain, request permission to-"

"Granted, Harry," she responded. "Go ahead and get some rest."

Ensign Kim left sickbay so that the others could get to work.

"Well, looks like somebody's got some de-evolving to do," Tom remarked, approaching the offspring.

"Will you be able to turn them into humans?" inquired Kes.

"Of course," said The Doctor, "But we should let you know, it is highly likely that in their human forms, they will be older than just a few days old."

"Why is that?" asked Janeway.

"A lot of non-humanoid species age faster than humans," Tom explained, "It appears as though these lizards are one of them."

"But their aging process should revert to normal once they are human," The Doctor reassured the two women.

Turning the offspring into humans was actually a fairly simple process. By combining Tom's advanced intellect with The Doctor's extensive medical knowledge, they were able to find a way to reverse the mutation process on the offspring. However, it had to be administered once at a time.

Tom and The Doctor administered the genetic sequencing on the first of the three children. Somehow, Tom could tell which was the eldest, which was the youngest, and which was the middle one, much to everyone's surprise.

The first offspring turned into a ten-month old baby girl. She had her mother's long brown hair, but her facial features were very similar to that of her father's. She was sound asleep at the time.

Tom handed the baby girl to Kes. Kes took her over to the main bio-bed, cleaned her up, and got a diaper from the replicator. After unfolding the diaper, she placed the sleeping baby on it. Kes pulled the diaper up firmly but gently between the baby's legs and fastened it at the sides. Then she wrapped her up securely in a blanket.

Captain Janeway watched Kes the whole time. When she saw the baby girl with her own two eyes, she felt an upswelling of love for her. She fully realized that this baby was not just any girl; she was her daughter!

Meanwhile, Tom and The Doctor had administered the genetic sequencing onto the second of the three offspring. This one turned into a ten-month old baby boy, who was also sound asleep. He was almost the opposite of his older sister: He had inherited his father's dark blonde hair, but he had his mother's facial features.

Tom handed his son to Kes. Kes cleaned him up, diapered him, and wrapped him up in another blanket.

Finally, Tom and The Doctor moved to the youngest of the offspring. This one was slightly smaller than the other two. After the genetic sequencing was administered, the result was another ten-month old baby girl. Her hair and facial features were a mix of her parents'. Unlike her sister and brother, she was awake during the process.

Tom smiled down at his daughter and said jovially "Welcome to the world."

The second baby girl tried to smile back, but she was unsuccessful. Tom handed her over to Kes. After she was cleaned, diapered, and wrapped up tight, Tom and Kathryn approached the main bio-bed.

Lying before them were three innocent lifes they had helped to create. Both of them felt a close connection to the three small children.

Still smiling, Tom turned to Janeway and said "Congratulations... Mom."

She turned to him, smiled in turn, and said "Congratulations to you, too... Dad."


	4. Plans Are Drawn

Note: Sorry about how long it's taken me to update. I've been focused on my Cats fanfic "Choices." I meant to update weeks ago, actually, but at the beginning of last month, I got into an accident on the highway. My car caught on fire and I lost everything I had inside, including my laptop, which had all my files for my fanfictions on it. Fortunately, everything was insured, so I had it all replaced for free (Including my car and laptop). Anyway, without further ado, I'll get on with the story.

The Doctor stepped up to the bio-bed to conduct a standard health examination of the _Voyager_'s three newest passengers.

He ran his tricorder over them, and something quite peculiar caught his eye.

"Hmmm…" he muttered as he double-checked the data he had acquired so far "I must say; this is rather peculiar."

"What is it, Doctor?" asked Janeway.

"Captain, the neural activity in these children's brains is well-above normal for their age," The Doctor reported to her, "In fact, when they start learning about the world, they will be almost as intelligent as Lieutenant Paris currently is."

"Wait a minute, Doc," said Tom, "Are you saying that these children are already able to process information about what they see and hear?"

"Yes, Lieutenant," The Doctor answered, "I would say that it will not be too long before they can learn how to walk, how to talk, how to sit up, and accomplish various other basic things. In fact, teaching them how to adapt as they get older will be relatively simple for whoever plans to take care of them."

"'Whoever plans to take care of them?'" repeated Tom. "Just what are you implying there, Doctor?"

"Well, Lieutenant, while you and the Captain are the children's biological parents, I know how busy the two of you can be," said The Doctor, "So I assumed that you would find someone to care for the children for you."

"Doc, I may be a goof and a jokester," Tom admitted, "But I am not immune to caring. While this may seem uncharacteristically noble of me, I fully intend to be a part of these children's lives."

"You're right, Lieutenant," said The Doctor, "That is uncharacteristically noble of you."

Tom turned to Janeway and said "Captain, I would like to submit a personal request."

"Very well, Lieutenant," she agreed.

"I would like to know which deck has the largest crew quarters available," said Tom, "And I would like to move to those said quarters."

"Why, Mr. Paris?" inquired the Captain.

"My current quarters are not nearly big enough," he enlightened her, "And if I'm going to take care of the children, I'm going to need-"

"Tom, forgive this interruption," said Janeway, "But you seem to be under the impression that you will take responsibility of these children by yourself."

"Well, shouldn't I be?" he asked.

Kathryn looked up at him with a mixed expression of disbelief and amusement. Then she said "No one should have to shoulder a challenge such as this one on their own."

Tom smiled; secretly, he was relieved that Captain Janeway was accepting this responsibility like him. He was sure that having someone with him would make such a concept of parenthood seem less difficult to carry out.

"I'm grateful for this, Captain," he smiled, "But there's still one problem. While your quarters are plenty big, mine are not. The way I see it, if the two of us are going to care for the children, we've only got two options: One, I get larger quarters – which you seem to have just denied – or two, both of us-"

Tom's facial expression froze as he realized what the Captain was implying. She just smirked and finished for him "'Move into the same room?' Well, that would certainly be the more convenient option."

Tom slowly but hesitantly nodded to acknowledge the logic in her statement. He was very fond of Kathryn Janeway, but the idea of sharing a room with her seemed rather odd to him.

"I actually believe that you and I can do this together, Tom," said Janeway, "What with the side-effects from the Threshold incident, I believe it can be done."

"Add that to the children's intelligence, one could say that you were 'cheating,'" commented The Doctor.

The others chuckled at his comment.

"That sounds like one of my lines, Doc," said Tom.

"Perhaps," The Doctor admitted.

…

By the end of the day, Janeway and Paris had gotten everything organized. Tom had gathered his possessions and moved into the Captain's quarters. Three small cribs had been added for the children, and a second bed had been added for Tom.

Tom was still a little nervous. The Captain could sense this from him with her new empathic abilities, and she decided to comfort him.

At the time, Tom was sitting on the couch, looking out the window into space. Kathryn sat down a few feet near him and asked him "Enjoying the view?"

"Quite," he replied, still focusing on the stars "I was always fascinated by them when I was younger. "

"I'll bet you were," she smiled at him and said "What about them incited your interest the most?"

Tom answered her: "Back when my father was still a Captain, my mother, my sisters, and I would sometimes travel with him on the ship he served. I would spend a long time watching and studying the stars. The thing I wondered the most was if we were really the ones that were moving, or if the stars themselves were moving and we were the one thing standing still. Have you ever wondered that, Captain?"

"As a matter of fact, I did," she answered, "Stars were always something of a mystery to me. But what's also a mystery to me at the moment is what is on your mind."

Tom turned to his Captain and said "I thought you were telepathic."

"No, I'm only telepathic every now and then," she reminded him, "But I am empathic. I can feel that you are under a lot of stress and anxiety. Tell me your thoughts, and I'll help you if I can."

"I hope you can," said Tom. He decided to be honest with her. He told her "I am somewhat worried about this whole 'parenthood' thing. Despite my intellect, I cannot help but wonder things like 'Will my children respect me, despite my history?' or 'Will they see me as a good role model?' or 'Can I actually do this?'"

"Well, based on the emotions I can sense from the children's minds when you're near them: absolutely yes, definitely yes, and I have no doubt," she answered his questions respectively.

"Well, despite that, there are still two other people I feel that I need to appease," Tom told Kathryn.

"Who would those people be?" she asked.

"You and I," he stated directly, "I'm worried that you'll be less than impressed in my role as father. I also don't think I could look myself in the mirror if I fail."

Kathryn took Tom's hands in hers and said "Tom, I want you to look me in the eyes."

He complied with her order. Once their eyes were focused on each other's, Kathryn said "I anticipate a great performance in your role as a father, so you do not need to worry about disappointing me. And I am sure you can look yourself in the mirror… because I am sure you will not fail. Just trust in yourself, and in me, and you will succeed."

He smiled at her again, and said "I love… how you always have the best advice whenever somebody needs it."

Their eyes remained connected for a moment longer, and then Tom said "Captain, I just remembered… we still have yet to name the children."

Kathryn realized this and said cheerily "I suggest that we do it as soon as possible."

The two of them sat thinking about ideal names for their son and their two daughters. They considered hundreds of different names before they finally agreed to three: Their elder daughter would be named Jessica ("Jessica Janeway-Paris" had a certain appeal to the two of them). Their son would be named Aaron (For one of Tom's best friends from his days at the academy). Lastly, their younger daughter would be named Wendy (For one of Kathryn's best friends from HER days at the academy).

After all that was settled, the two of them went to work organizing their plans for both the near and far future.


End file.
